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The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.

During female germline development, oocytes become a highly specialized cell type and form a maternal cytoplasmic store of crucial factors. Oocyte growth is triggered at the transition from primordial to primary follicle and is accompanied by dynamic changes in gene expression1, but the gene regulatory network that controls oocyte growth remains unknown. Here we identify a set of transcription factors that are sufficient to trigger oocyte growth. By investigation of the changes in gene expression and functional screening using an in vitro mouse oocyte development system, we identified eight transcription factors, each of which was essential for the transition from primordial to primary follicle. Notably, enforced expression of these transcription factors swiftly converted pluripotent stem cells into oocyte-like cells that were competent for fertilization and subsequent cleavage. These transcription-factor-induced oocyte-like cells were formed without specification of primordial germ cells, epigenetic reprogramming or meiosis, and demonstrate that oocyte growth and lineage-specific de novo DNA methylation are separable from the preceding epigenetic reprogramming in primordial germ cells. This study identifies a core set of transcription factors for orchestrating oocyte growth, and provides an alternative source of ooplasm, which is a unique material for reproductive biology and medicine. Eight transcription factors are identified that, when overexpressed, are sufficient to grow oocyte-like cells from mouse pluripotent stem cells.

Summary The first-in-human trial of induced pluripotent stem cell (iPSC)-based autologous transplantation was successfully performed on a female patient with age-related macular degeneration. Here we delineated the base-resolution methylome of the iPSC-derived retinal pigment epithelium (iRPE) used in this trial. The methylome of iRPE closely resembled that of native RPE (nRPE), although partially methylated domains (PMDs) emerged in iRPE but not nRPE. Most differentially methylated regions between iRPE and nRPE appeared to originate from (de)methylation errors during differentiation, whereas errors at reprogramming resulted in aberrant genomic imprinting and X chromosome reactivation. Moreover, non-CpG methylation was prominent in nRPE but not iRPE. Intriguingly, xenotransplantation to mouse remodeled the iRPE methylome to demethylate a subset of suppressed genes and accumulate non-CpG methylation, but failed to resolve PMDs and hypermethylated CpG islands. Although the impacts of these alterations remain elusive, our findings should provide a useful guide for methylome analyses of other iPSC-derived cells., Highlights • The methylome of iPSC-derived RPE closely resembled that of native RPE • Most methylomic differences originated from errors during differentiation • Errors at reprogramming induced loss of imprinting and X chromosome reactivation • Some of the differences were mitigated by xenotransplantation to mouse, In this article, Ito and colleagues delineated the base-resolution methylome of iPSC-derived retinal pigment epithelial (RPE) cell used in the first-in-human trial of autologous transplantation. The methylome closely resembled that of native RPE cell. Intriguingly, it became even closer to its natural counterpart upon xenotransplantation to mouse, demonstrating its plasticity to respond appropriately to the in vivo environment.

Adult muscles and their associated stem cells retain functional positional memory based on developmental origin., Muscle stem cells (satellite cells) are distributed throughout the body and have heterogeneous properties among muscles. However, functional topographical genes in satellite cells of adult muscle remain unidentified. Here, we show that expression of Homeobox-A (Hox-A) cluster genes accompanied with DNA hypermethylation of the Hox-A locus was robustly maintained in both somite-derived muscles and their associated satellite cells in adult mice, which recapitulates their embryonic origin. Somite-derived satellite cells were clearly separated from cells derived from cranial mesoderm in Hoxa10 expression. Hoxa10 inactivation led to genomic instability and mitotic catastrophe in somite-derived satellite cells in mice and human. Satellite cell–specific Hoxa10 ablation in mice resulted in a decline in the regenerative ability of somite-derived muscles, which were unobserved in cranial mesoderm–derived muscles. Thus, our results show that Hox gene expression profiles instill the embryonic history in satellite cells as positional memory, potentially modulating region-specific pathophysiology in adult muscles.

The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.

Macrophage-like cells derived from vascular smooth muscle cells (SMCs) play critical roles in atherogenesis, and DNA hydroxymethylation was implicated in transdifferentiation. We examined transcriptomes and (hydroxy)methylomes of human coronary artery SMCs during cholesterol-induced transdifferentiation. A unique approach of exhaustive identification of differentially expressed genes followed by Gene Ontology-centric clustering facilitated deeper understanding of multifaceted modulations of genes involved in extracellular matrix organization, angiogenesis, cell migration, hypoxia response, and cholesterol biosynthesis. Intriguingly, type I interferon response was transiently activated, presumably forming an immuno-metabolic circuit with cholesterol metabolism. Neither global nor DEG-proximal changes were evident in (hydroxy)methylation. These results would not only provide a unique data resource for atherosclerosis research but present a potentially useful approach in transcriptome data interpretation., Highlights • Cholesterol-induced transcriptome dynamics revealed in human vascular SMCs. • Type I interferon response transiently activated in cholesterol-loaded SMCs. • Interpretation of transcriptome dynamics facilitated by GO-centric clustering.

Ageing of the uterine endometrium is a critical factor that affects reproductive success, but the mechanisms associated with uterine ageing are unclear. In this study, we conducted a qualitative examination of age-related changes in endometrial tissues and identified candidate genes as markers for uterine ageing. Gene expression patterns were assessed by two RNA-sequencing experiments using uterine tissues from wild type (WT) C57BL/6 mice. Gene expression data obtained by RNA-sequencing were validated by real-time PCR. Genes expressing the pro-inflammatory cytokines Il17rb and chemokines Cxcl12 and Cxcl14 showed differential expression between aged WT mice and a group of mice composed of 5- and 8-week-old WT (young) animals. Protein expression levels of the above-mentioned genes and of IL8, which functions downstream of IL17RB, were analysed by quantitative immunohistochemistry of unaffected human endometrium tissue samples from patients in their 20s and 40s (10 cases each). In the secretory phase samples, 3,3ʹ- diaminobenzidine staining intensities of IL17RB, CXCL12 and CXCL14 for patients in their 40s were significantly higher than that for patients in their 20s, as detected by a Mann–hitney U test. These results suggest that these genes are candidate markers for endometrial ageing and for prediction of age-related infertility, although confirmation of these findings is needed in larger studies involving fertile and infertile women.

Background Apoptosis is a critical process in endothelial cell (EC) biology and pathology, which has been extensively studied at protein level. Numerous gene expression studies of EC apoptosis have also been performed, however few attempts have been made to use gene expression data to identify the molecular relationships and master regulators that underlie EC apoptosis. Therefore, we sought to understand these relationships by generating a Bayesian gene regulatory network (GRN) model. Results ECs were induced to undergo apoptosis using serum withdrawal and followed over a time course in triplicate, using microarrays. When generating the GRN, this EC time course data was supplemented by a library of microarray data from EC treated with siRNAs targeting over 350 signalling molecules. The GRN model proposed Vasohibin-1 (VASH1) as one of the candidate master-regulators of EC apoptosis with numerous downstream mRNAs. To evaluate the role played by VASH1 in EC, we used siRNA to reduce the expression of VASH1. Of 10 mRNAs downstream of VASH1 in the GRN that were examined, 7 were significantly up- or down-regulated in the direction predicted by the GRN.Further supporting an important biological role of VASH1 in EC, targeted reduction of VASH1 mRNA abundance conferred resistance to serum withdrawal-induced EC death. Conclusion We have utilised Bayesian GRN modelling to identify a novel candidate master regulator of EC apoptosis. This study demonstrates how GRN technology can complement traditional methods to hypothesise the regulatory relationships that underlie important biological processes.

Two recurrent mutations, K27M and G34R/V, in H3F3A, encoding non-canonical histone H3.3, are reported in pediatric and young adult gliomas, whereas G34W mutation is prevalent in bone tumors. In contrast to K27M mutation, it remains elusive how G34 mutations affect the epigenome. Here we performed whole-genome bisulfite sequencing of four G34R-mutated gliomas and the G34V-mutated glioma cell line KNS-42 for comparison with gliomas harboring K27M and no mutations in H3F3A and with G34W-mutated bone tumors. G34R-mutated gliomas exhibited lower global methylation levels, similar CpG island (CGI) methylation levels, and compromised hypermethylation of telomere-proximal CGIs, compared to the other two glioma subgroups. Hypermethylated regions specific to G34R-mutated gliomas were enriched for CGIs, including those of OLIG1, OLIG2, and canonical histone genes in the HIST1 cluster. They were notably hypermethylated in osteosarcomas with, but not without, G34W mutation. Independent component analysis revealed that G34 mutation-specific components shared a significant similarity between glioma and osteosarcoma, suggesting that G34 mutations exert characteristic methylomic effects regardless of the tumor tissue-of-origin. CRISPR/Cas9-mediated disruption of G34V-allele in KNS-42 cells led to demethylation of a subset of CGIs hypermethylated in G34R-mutated gliomas. These findings will provide a basis for elucidating epigenomic roles of G34 oncohistone in tumorigenesis.

A contribution of epigenetic modifications to B cell tolerance has been proposed but not directly tested. Here we report that deficiency of ten-eleven translocation (Tet) DNA demethylase family members Tet2 and Tet3 in B cells led to hyperactivation of B and T cells, autoantibody production and lupus-like disease in mice. Mechanistically, in the absence of Tet2 and Tet3, downregulation of CD86, which normally occurs following chronic exposure of self-reactive B cells to self-antigen, did not take place. The importance of dysregulated CD86 expression in Tet2- and Tet3-deficient B cells was further demonstrated by the restriction, albeit not complete, on aberrant T and B cell activation following anti-CD86 blockade. Tet2- and Tet3-deficient B cells had decreased accumulation of histone deacetylase 1 (HDAC1) and HDAC2 at the Cd86 locus. Thus, our findings suggest that Tet2- and Tet3-mediated chromatin modification participates in repression of CD86 on chronically stimulated self-reactive B cells, which contributes, at least in part, to preventing autoimmunity.

Whole-genome bisulfite sequencing (WGBS) is the current gold standard of methylome analysis. Post-bisulfite adaptor tagging (PBAT) is an increasingly popular WGBS protocol because of high sensitivity and low bias. PBAT originally relied on two rounds of random priming for adaptor-tagging of single-stranded DNA (ssDNA) to attain high efficiency but at a cost of library insert length. To overcome this limitation, we developed terminal deoxyribonucleotidyl transferase (TdT)-assisted adenylate connector-mediated ssDNA (TACS) ligation as an alternative to random priming. In this method, TdT attaches adenylates to the 3′-end of input ssDNA, which are then utilized by RNA ligase as an efficient connector to the ssDNA adaptor. A protocol that uses TACS ligation instead of the second random priming step substantially increased the lengths of PBAT library fragments. Moreover, we devised a dual-library strategy that splits the input DNA to prepare two libraries with reciprocal adaptor polarity, combining them prior to sequencing. This strategy ensured an ideal base–color balance to eliminate the need for DNA spike-in for color compensation, further improving the throughput and quality of WGBS. Adopting the above strategies to the HiSeq X Ten and NovaSeq 6000 platforms, we established a cost-effective, high-quality WGBS, which should accelerate various methylome analyses.

We propose a simple gradation representation method using a binary-weighted computer-generated hologram (CGH) to be displayed on a high-speed spatial light modulator that can be controlled by the pulse-width modulation technique. The proposed method uses multiple bit planes comprising binary-weighted CGHs with various pulse widths. The object points of a three-dimensional (3D) object are assigned to multiple bit planes according to their gray levels. The bit planes are sequentially displayed in a time-division-multiplexed manner. Consequently, the proposed method realizes a gradation representation of a reconstructed 3D object.

BACKGROUND Two recurrent mutations, K27M and G34R/V, in H3F3A, encoding non-canonical histone H3.3, are reported in pediatric and young adult gliomas, whereas G34W mutation was prevalent in bone tumors. In contrast to K27 mutation, it remains elusive how G34 mutations affect the epigenome. Here we performed whole-genome bisulfite sequencing of four G34R-mutated gliomas and the G34V-mutated glioma cell line KNS-42. Similarly, we analyzed seven and three gliomas harboring K27M and no mutations in H3F3A, respectively. These data were compared with those on bone tumors. RESULTS G34R-mutated gliomas exhibited lower global methylation levels, similar CpG island (CGI) methylation levels, and compromised hypermethylation of telomere-proximal CGIs compared with those bearing K27M and no mutations. Hypermethylated regions specific to G34R-mutated gliomas were enriched for CGIs, including those of OLIG1, OLIG2, and canonical histone genes in the HIST1 cluster. These CGIs were hypermethylated in osteosarcomas with, but not without, the G34W mutation. In KNS-42 cells, CGIs with G34V-mutated histone H3.3 exhibited higher methylation levels than those with wild-type histone H3.3. This effect was also observed in the G34R-mutated glioma samples. CONCLUSIONS Gliomas bearing G34R/V mutations display characteristic methylomic alterations, some of which are shared by osteosarcomas with the G34W mutation. Deposition of G34 variants may lead to elevated methylation of otherwise hypomethylated, histone H3.3-bearing CGIs.

Summary Paternal dietary conditions may contribute to metabolic disorders in offspring. We have analyzed the role of the stress-dependent epigenetic regulator cyclic AMP-dependent transcription factor 7 (ATF7) in paternal low-protein diet (pLPD)-induced gene expression changes in mouse liver. Atf7+/– mutations cause an offspring phenotype similar to that caused by pLPD, and the effect of pLPD almost vanished when paternal Atf7+/– mice were used. ATF7 binds to the promoter regions of ∼2,300 genes, including cholesterol biosynthesis-related and tRNA genes in testicular germ cells (TGCs). LPD induces ATF7 phosphorylation by p38 via reactive oxygen species (ROS) in TGCs. This leads to the release of ATF7 and a decrease in histone H3K9 dimethylation (H3K9me2) on its target genes. These epigenetic changes are maintained and induce expression of some tRNA fragments in spermatozoa. These results indicate that LPD-induced and ATF7-dependent epigenetic changes in TGCs play an important role in paternal diet-induced metabolic reprograming in offspring.

The majority of histones are replaced by protamines during spermatogenesis, but small amounts are retained in mammalian spermatozoa. Since nucleosomes in spermatozoa influence epigenetic inheritance, it is important to know how histones are distributed in the sperm genome. Conflicting data, which may result from different conditions used for micrococcal nuclease (MNase) digestion, have been reported: retention of nucleosomes at either gene promoter regions or within distal gene-poor regions. Here, we find that the swim-up sperm used in many studies contain about 10% population of sperm which have not yet completed the histone-to-protamine replacement. We develop a method to purify histone replacement-completed sperm (HRCS) and to completely solubilize histones from cross-linked HRCS without MNase digestion. Our results indicate that histones are retained at specific promoter regions in HRCS. This method allows the study of epigenetic status in mature sperm.

The rate of gas exchange in plants is regulated mainly by stomatal size and density. Generally, higher densities of smaller stomata are advantageous for gas exchange; however, it is unclear what the effect of an extraordinary change in stomatal size might have on a plant’s gas-exchange capacity. We investigated the stomatal responses to CO2 concentration changes among 374 Arabidopsis (Arabidopsis thaliana) ecotypes and discovered that Mechtshausen (Me-0), a natural tetraploid ecotype, has significantly larger stomata and can achieve a high stomatal conductance. We surmised that the cause of the increased stomatal conductance is tetraploidization; however, the stomatal conductance of another tetraploid accession, tetraploid Columbia (Col), was not as high as that in Me-0. One difference between these two accessions was the size of their stomatal apertures. Analyses of abscisic acid sensitivity, ion balance, and gene expression profiles suggested that physiological or genetic factors restrict the stomatal opening in tetraploid Col but not in Me-0. Our results show that Me-0 overcomes the handicap of stomatal opening that is typical for tetraploids and achieves higher stomatal conductance compared with the closely related tetraploid Col on account of larger stomatal apertures. This study provides evidence for whether larger stomatal size in tetraploids of higher plants can improve stomatal conductance.

Personalized peptide vaccination (PPV) is an attractive approach to cancer immunotherapy with strong immune-boosting effects conferring significant clinical benefit. However, as with most therapeutic agents, there is a difference in clinical efficacy among patients receiving PPV. Therefore, a useful biomarker is urgently needed for prognosticating clinical outcomes to preselect patients who would benefit the most from PPV. In this retrospective study, to detect a molecular prognosticator of clinical outcomes for PPV, we analyzed whole-genome gene expression profiles of peripheral blood mononuclear cells (PBMCs) in castration-resistant prostate cancer (CRPC) patients before administration of PPV. Cox regression analysis revealed that mRNA expression of myeloperoxidase, haptoglobin, and neutrophil elastase was significantly associated with overall survival (OS) among vaccinated CRPC patients (adjusted P

We demonstrate real-time three-dimensional (3D) color video using a color electroholographic system with a cluster of multiple-graphics processing units (multi-GPU) and three spatial light modulators (SLMs) corresponding respectively to red, green, and blue (RGB)-colored reconstructing lights. The multi-GPU cluster has a computer-generated hologram (CGH) display node containing a GPU, for displaying calculated CGHs on SLMs, and four CGH calculation nodes using 12 GPUs. The GPUs in the CGH calculation node generate CGHs corresponding to RGB reconstructing lights in a 3D color video using pipeline processing. Real-time color electroholography was realized for a 3D color object comprising approximately 21,000 points per color.

Reliable predictors of tumor recurrence for patients with stage II colorectal cancer (CRC) are needed to select patients who should receive adjuvant chemotherapy. Although galanin (GAL) is expressed in several malignant tumors and is associated with cell proliferation and tumor growth, the prognostic value of GAL expression in CRC is poorly understood. We compared GAL expression between 56 patients with stage II and III CRC who developed tumor recurrences and 56 patients who did not. The clinical and prognostic significance of GAL expression was examined using our data and independent public datasets. We also analyzed the influence of GAL expression on the proliferation and invasive activity of CRC cells. Higher expression of GAL was associated with tumor recurrence among the CRC patients (P

A highly efficient OLED lighting product using all-phosphorescent technology, for the first time in the world, is presented. Using proprietary blue phosphorescent emitter, 45 lm/W white emission is achieved at 2800K color temperature. The produced panel has very low driving voltage and small color shift regarding the viewing angle. The successful commercialization of all-phosphorescent technology would bring great power saving feature for OLED to compete with other technologies.

Highlights ► Gene Set Analysis (GSA) can reveal biological meaning from “omics” experiments. ► It is currently difficult to apply GSA to the range of available gene set databases. ► We constructed GeneSetDB, a comprehensive meta-database for gene set analysis. ► GeneSetDB integrates 26 databases containing different types of information. ► GeneSetDB lets biologists visualise the gene sets represented in their “omics” results., Most “omics” experiments require comprehensive interpretation of the biological meaning of gene lists. To address this requirement, a number of gene set analysis (GSA) tools have been developed. Although the biological value of GSA is strictly limited by the breadth of the gene sets used, very few methods exist for simultaneously analysing multiple publically available gene set databases. Therefore, we constructed GeneSetDB (http://genesetdb.auckland.ac.nz/haeremai.html), a comprehensive meta-database, which integrates 26 public databases containing diverse biological information with a particular focus on human disease and pharmacology. GeneSetDB enables users to search for gene sets containing a gene identifier or keyword, generate their own gene sets, or statistically test for enrichment of an uploaded gene list across all gene sets, and visualise gene set enrichment and overlap using a clustered heat map.

In the post-genome era, with the availability of high-throughput data, our biological focus makes a shift from a behavior of individual components to their regulatory/causative/interactive relationships. Gene network, which is inferred from microarray data by using reverse engineering algorithms, gives valuable information about the regulation of genes in the living cells under the certain conditions. In particular, this technology is applied to the biomedical research fields, e.g. identification of drug targets and prognosis markers. In this short review, we summarize what gene network is and how it is inferred. We also show our work that identified new drug target of well-known compound in human endothelial cells by gene network analysis.

We propose real-time time-division color electroholography using a single graphics processing unit (GPU) and a simple synchronization system of reference light. To facilitate real-time time-division color electroholography, we developed a light emitting diode (LED) controller with a universal serial bus (USB) module and the drive circuit for reference light. A one-chip RGB LED connected to a personal computer via an LED controller was used as the reference light. A single GPU calculates three computer-generated holograms (CGHs) suitable for red, green, and blue colors in each frame of a three-dimensional (3D) movie. After CGH calculation using a single GPU, the CPU can synchronize the CGH display with the color switching of the one-chip RGB LED via the LED controller. Consequently, we succeeded in real-time time-division color electroholography for a 3D object consisting of around 1000 points per color when an NVIDIA GeForce GTX TITAN was used as the GPU. Furthermore, we implemented the proposed method in various GPUs. The experimental results showed that the proposed method was effective for various GPUs.

Endothelial cell (EC) apoptosis may play an important role in blood vessel development, homeostasis and remodelling. In support of this concept, EC apoptosis has been detected within remodelling vesselsin vivo, and inactivation of EC apoptosis regulators has caused dramatic vascular phenotypes. EC apoptosis has also been associated with cardiovascular pathologies. Therefore, understanding the regulation of EC apoptosis, with the goal of intervening in this process, has become a current research focus. The protein-based signalling and cleavage cascades that regulate EC apoptosis are well known. However, the possibility that programmed transcriptome and glycome changes contribute to EC apoptosis has only recently been explored. Traditional bioinformatic techniques have allowed simultaneous study of thousands of molecular signals during the process of EC apoptosis. However, to progress further, we now need to understand the complex cause and effect relationships among these signals. In this article, we will first review current knowledge about the function and regulation of EC apoptosis including the roles of the proteome transcriptome and glycome. Then, we assess the potential for further bioinformatic analysis to advance our understanding of EC apoptosis, including the limitations of current technologies and the potential of emerging technologies such as gene regulatory networks.

Background Base-resolution methylome data generated by whole-genome bisulfite sequencing (WGBS) is often used to segment the genome into domains with distinct methylation levels. However, most segmentation methods include many parameters to be carefully tuned and/or fail to exploit the unsurpassed resolution of the data. Furthermore, there is no simple method that displays the composition of the domains to grasp global trends in each methylome. Results We propose to use changepoint detection for domain demarcation based on base-resolution methylome data. While the proposed method segments the methylome in a largely comparable manner to conventional approaches, it has only a single parameter to be tuned. Furthermore, it fully exploits the base-resolution of the data to enable simultaneous detection of methylation changes in even contrasting size ranges, such as focal hypermethylation and global hypomethylation in cancer methylomes. We also propose a simple plot termed methylated domain landscape (MDL) that globally displays the size, the methylation level and the number of the domains thus defined, thereby enabling one to intuitively grasp trends in each methylome. Since the pattern of MDL often reflects cell lineages and is largely unaffected by data size, it can serve as a novel signature of methylome. Conclusions Changepoint detection in base-resolution methylome data followed by MDL plotting provides a novel method for methylome characterization and will facilitate global comparison among various WGBS data differing in size and even species origin. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1809-5) contains supplementary material, which is available to authorized users.

We propose a method for color electroholography using a simple red–green–blue (RGB) gradation representation method without controlling the respective brightness of the reference RGB-colored lights. The proposed method uses RGB multiple bit planes comprising RGB binary-weighted computer-generated holograms with various light transmittances. The object points of a given three-dimensional (3D) object are assigned to RGB multiple bit planes according to their RGB gradation levels. The RGB multiple bit planes are sequentially displayed in a time-division-multiplexed manner. Consequently, the proposed method yields a color gradation representation of a reconstructed 3D object.

We propose a real-time spatiotemporal division multiplexing electroholography utilizing the features of movies. The proposed method spatially divides a 3-D object into plural parts and periodically selects a divided part in each frame, thereby reconstructing a three-dimensional (3-D) movie of the original object. Computer-generated holograms of the selected part are calculated by a single graphics processing unit and sequentially displayed on a spatial light modulator. Visual continuity enables a reconstructed movie of the original 3-D object. The proposed method realized a real-time reconstructed movie of a 3-D object composed of 11,646 points at over 30 frames per second (fps). We also displayed a reconstructed movie of a 3-D object composed of 44,647 points at about 10 fps.

Because of the complexity arising from the large molecular size and the amino acid sequence homologies of IgG-binding domains of Staphylococcal Protein A (SpA), we have introduced, a combination of stable isotope labeling and both qualitative and quantitative investigations of the structural dependence of the NMR chemical shifts for its structure analysis. In order to enable selective isotope labeling with high efficiency, a mutated low molecular weight Protein A (LPA; MWt = 27 kDa) which consists of E, D, A, B and 13 residues of the C-domain was used in this study. Amide proton chemical shifts, measured using uniformly 15N-labeled LPA and LPA labeled selectively with 15N-alanine, show that the turn between helices 1 and 2, and its tertiary interactions with helix 3, are very similar in all domains. This contradicts previous results obtained using independent structure calculations on isolated domains. The close similarity in NH and 15N chemical shifts of alanine residues in the interdomain linker suggests that the linker maintains a similar structure both in isolated domains and in the intact protein. We show that the high-field shifted methyl signal of Ala 48 is affected by the ring-current effect arising from Phe 30, and has a very similar helical environment in all four domains. Thus, helix 3 is present in all domains, as we previously reported [Kikuchi et al., J Biochem Biophys Method, 1999:38:203-208], even though it is not observed in the crystal structure [Deisenhofer J. Biochemistry 1981;20:2361-2370].

We propose a simple gradation representation method for a reconstructed three-dimensional (3-D) image without controlling the brightness of the reference light. In the proposed method, we use multiple bit planes comprised of binary-weighted computer-generated holograms (CGHs) with various light transmittances. Binary-weighted CGH is generated by changing the white in the conventional binary CGH to gray. The light transmittance of a binary-weighted CGH is less than that of a conventional binary CGH. The object points of a 3-D object are assigned to multiple bit planes according to the gray level of the object points. The multiple bit planes are displayed sequentially in a time-division multiplex manner. Consequently, the proposed method realizes a gradation representation of a reconstructed 3-D object.

We demonstrate fast time-division color electroholography using a multiple-graphics-processing-unit (GPU) cluster system with a spatial light modulator and a controller to switch the color of the reconstructing light. The controller comprises a universal serial bus module to drive the liquid crystal optical shutters. By using the controller, the computer-generated hologram (CGH) display node of the multiple-GPU cluster system synchronizes the display of the CGH with the color switching of the reconstructing light. Fast time-division color electroholography at 20 fps is realized for a three-dimensional object comprising 21,000 points per color when 13 GPUs are used in a multiple-GPU cluster system.

Parallel calculations of large-pixel-count computer-generated holograms (CGHs) are suitable for multiple-graphics processing unit (multi-GPU) cluster systems. However, it is not easy for a multi-GPU cluster system to accomplish fast CGH calculations when CGH transfers between PCs are required. In these cases, the CGH transfer between the PCs becomes a bottleneck. Usually, this problem occurs only in multi-GPU cluster systems with a single spatial light modulator. To overcome this problem, we propose a simple method using the InfiniBand network. The computational speed of the proposed method using 13 GPUs (NVIDIA GeForce GTX TITAN X) was more than 3000 times faster than that of a CPU (Intel Core i7 4770) when the number of three-dimensional (3-D) object points exceeded 20,480. In practice, we achieved ∼40 tera floating point operations per second (TFLOPS) when the number of 3-D object points exceeded 40,960. Our proposed method was able to reconstruct a real-time movie of a 3-D object comprising 95,949 points.

Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions.